SAXSdb — 8kdz

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1. Protein Identity and Related Structures Protein Identity & Related Structures

methyltransferase

dengue virus type 3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	S-ADENOSYL-L-HOMOCYSTEINE × 2 2-phenylethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C1KBQ3_9FLAV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–284； UniProt 2491–2755 Author chain B； PDBConstruct 20–284； UniProt 2491–2755

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8kdz
Deposition date deposition_date	2023-08-10
Structure title title	DENGUE 3 NS5 METHYLTRANSFERASE BOUND TO S-Adenosyl-L-homocysteine and Caffeic acid phenethyl ester
Keywords keywords	Inhibitor, Methyltransferase, Dengue 3, Antiviral, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8kdz__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8kdz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8kdz__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	27.67 Å
Rg (electron density)	26.84 Å
Total Rg	27.57 Å
Atom count	4178
Residues	512
Excluded volume	74408 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8kdz__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	methyltransferase
Molecular weight formula_weight	32107.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4302

HHHHHHSSGLVPRGSHMASGTGSQGETLGEKWKKKLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGETTHHAVSRGSAKLQWFVERNMVIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTKGGPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDIGESSPSPTVEESRTIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLVRNPLSRNSTHEMYWISNGTGNIVSSVNMVSRLLLNRFTMTHRRPTIEKDVDLGAGTRHVN

Source Source

Source organism organism	dengue virus type 3
NCBI taxonomy ID ncbi_taxonomy_id	11069
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	2-phenylethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate
Molecular weight formula_weight	284.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	124

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Unit-cell length a length_a	51.648 Å
Unit-cell length b length_b	60.722 Å
Unit-cell length c length_c	184.360 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	23.056 Å
R factor r_factor	—
R_work r_work	0.2310
R_free r_free	0.2727

DENGUE 3 NS5 METHYLTRANSFERASE BOUND TO S-Adenosyl-L-homocysteine and Caffeic acid phenethyl ester

1. Protein Identity and Related Structures Protein Identity & Related Structures

methyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8kdz__assembly_1__model_1

8kdz__assembly_1__model_1 | I(q)

8kdz__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

DENGUE 3 NS5 METHYLTRANSFERASE BOUND TO S-Adenosyl-L-homocysteine and Caffeic acid phenethyl ester

1. Protein Identity and Related Structures Protein Identity & Related Structures

methyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8kdz__assembly_1__model_1

8kdz__assembly_1__model_1 | I(q)

8kdz__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)